Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Chain helicity

Semiempirical, ab initio, and density functional theory (DFT) studies were conducted on a homologous series of straight chain perfluoroalkyl carboxylic acids (PFCAs) ranging in chain length from C~1~ (trifluoroacetic acid; TFA) to C~9~ (perfluorodecanoic acid). Regardless of perfluoroalkyl chain length and computational method and level employed, no significant change in the electrostatic or steric characteristics of the carboxylate head group was found between C~2~ and C~9~. Application of a thermodynamic cycle to calculations at the B3LYP/6-311++G(3df,2p) level provided an accurate prediction of the experimental monomeric pK~a~ for TFA. At this – and similar – levels of theory, monomeric pK~a~ values of longer straight chain PFCAs are expected to display no significant increase with increasing chain length, having a relatively constant pK~a~ value of about 0 that is in excellent agreement with earlier predictions and with recent experimental evidence. Contrary to previous claims, perfluoroalkyl chain helicity does not appear to result in increased monomeric PFCA pK~a~ values at chain lengths >5 perfluorocarbons

A PHYSICAL CHEMIST'S GUIDE TO APPLIED COMPUTATIONAL CHEMISTRY: PRACTICAL CALCULATION OF POLYPROTIC ACID PKA VALUES, MERCURY HALIDES, THIOLS, AND METHYLMERCURY ANALOGUES' STABILITIES AND STRUCTURES, AND RAMAN SPECTRA OF MYO-INOSITOL HEXAKIS PHOSPHATE.

In this thesis, we present both ab-initio investigation of the series of compounds HgClxy and the charges of each system running x=(0,1,2,3,4) and y=(+2,+1,0,-1,-2). We investigate the energies of formation using Gaussian 03 (G03), a quantum chemistry package. In our calculations, HgCl3-1 was most stable in the gas phase, and HgCl20 the most stable in the polarizable continuum model water-solvated phase. The addition of a solvent layer of H2O molecules did not significantly affect the results. DFT calculations on the series running between HgCl+, through HgCl20, and HgCl3-1 compounds done with the Amsterdam Density Functional (ADF) program from Scientific Computing and Modeling (SCM) yielded absolute Hg NMR shieldings with a Δ of approximately -1000 ppm for each additional atom of Chlorine bonding to the Mercury for the first two additions. We also investigate H3PO4, H3AsO4, and the HClOx acid series with x=(1,2,3,4). We have succeeded in determining pKas with theoretical quality results within 2 kcal/mol of experimental measurement for the majority of the systems examined by use of a discovered linear correlation between experimental and calculated pKa values. Finally, we present our contribution to a joint project involving myo-inositol hexakis phosphate with an experimental group, confirming the observed experimental trends seen in the Raman spectra

Computational Methods in Biomolecules:Study of Hydrophilic Interactions in Protein Folding & Constant-pH Molecular Simulation of pH Sensitive Lipid MORC16

Water molecules play a significant role in biological process and are directly involved with bio-molecules and organic compounds and ions. Recent research has focused on the thermal dynamics and kinetics of water molecules in solution, including experimental (infrared spectroscopy and Raman spectroscopy) and computational (Quantum Mechanics and Molecular Dynamics) approaches. The reason that water molecules are so unique, why they have such a profound influence on bio-activity, why water molecules show some anomalies compared to other small molecules, and where and how water molecules exert their influence on solutes are some of the areas under study. We studied some properties of hydrogen bond networks, and the relationship of these properties with solutes in water. Molecular dynamics simulation, followed by an analysis of “water bridges”, which represent protein-water interaction have been carried out on folded and unfolded proteins. Results suggest that the formation of transient water bridges within a certain distance helps to consolidate the protein, possibly in transition states, and may help further guide the correct folding of proteins from these transition states. This is supporting evidence that a hydrophilic interaction is the driving force of protein folding. Biological membranes are complex structures formed mostly by lipids and proteins. For this reason the lipid bilayer has received much attention, through computation and experimental studies in recent years. In this dissertation, we report results of a newly designed pH sensitive lipid MORC16, through all-atom and coarse-grained models. The results did not yield a MORC16 amphiphile which flips its conformation in response to protonation. This may be due to imperfect force field parameters for this lipid, an imperfect protonation definition, or formation of hydrogen bond does not responsible for conformation flip in our models. Despite this, some insights for future work were obtained

Inhibition mechanism of the chloride channel TMEM16A by the pore blocker 1PBC

TMEM16A, a calcium-activated chloride channel involved in multiple cellular processes, is a proposed target for diseases such as hypertension, asthma, and cystic fibrosis. Despite these therapeutic promises, its pharmacology remains poorly understood. Here, we present a cryo-EM structure of TMEM16A in complex with the channel blocker 1PBC and a detailed functional analysis of its inhibition mechanism. A pocket located external to the neck region of the hourglass-shaped pore is responsible for open-channel block by 1PBC and presumably also by its structural analogs. The binding of the blocker stabilizes an open-like conformation of the channel that involves a rearrangement of several pore helices. The expansion of the outer pore enhances blocker sensitivity and enables 1PBC to bind at a site within the transmembrane electric field. Our results define the mechanism of inhibition and gating and will facilitate the design of new, potent TMEM16A modulators

Recovery of Ionic Liquids from aqueous solution by Nanofiltration

The T-SAR methodology was combined with membrane characterization methods. An application of the combined approach was demonstrated with two commercial nanofiltration membranes and it was possible to successfully predict their performance for the recovery of ionic liquids from aqueous solution. Using model solutions of Pyr16 (CF3SO2)2N, it could be evidenced the formation of a new phase of ionic liquid during the concentration process. In this case, 66% of the ionic liquid was separated and the effective recovery rate was duplicated up to 30% by using a coalescence filter. Hydrophobic ionic liquids from wastewaters produced in biotransformations of 2-octanone to 2-octanol, could be recovered as a separate phase, but hydrophilic ionic liquids which are used for the dissolution of cellulose and its subsequent regeneration could be only recovered as an aqueous solution. Recommendations for the systematic recovery of ionic liquids from industrial wastewaters were also introduced

Evidence of Hydrocarbon-Rich Fluid Interaction with Clays: Clay Mineralogy and Boron Isotope Data from Gulf of Cádiz Mud Volcano Sediments

Clay dehydration at great depth generates fluids and overpressures in organic-rich sediments that can release isotopically light boron from mature organic matter, producing 10B-rich fluids. The B can be incorporated into the tetrahedral sites of authigenic illite during the illitization of smectite. Therefore, the crystal-chemical and geochemical characterization of illite, smectite or interlayered illite–smectite clay minerals can be an indicator of depth (temperature) and reactions with the basin fluids. The aim of this study was to determine the detailed clay mineralogy, B-content and isotopic composition in illite–smectite rich samples of mud volcanoes from the Gulf of Cádiz, in order to evaluate interactions of hydrocarbon-rich fluids with clays. Molecular modeling of the illite structure was performed, using electron density functional theory (DFT) methods to examine the phenomenon of B incorporation into illite at the atomic level. We found that it is energetically preferable for B to reside in the tetrahedral sites replacing Si atoms than in the interlayer of expandable clays. The B abundances in this study are high and consistent with previous results of B data on interstitial fluids, suggesting that hydrocarbon-related fluids approaching temperatures of methane generation (150 C) are the likely source of B-rich illite in the studied samples